update one-sided fisher test to two-sided

core/src/main/java/org/mskcc/cbio/portal/servlet/CalcFisherExactTest.java

@@ -44,13 +44,13 @@
 import org.mskcc.cbio.portal.stats.FisherExact;
 
 /**
- * Calculate the cumulative (one-tail) p-value out of fisher exact test
+ * Calculate the cumulative (two-tail) p-value out of fisher exact test
  * 
  * @param a a, b, c, d are the four cells in a 2x2 matrix
  * @param b
  * @param c
  * @param d
- * @return one-tailed P-value (right or left, whichever is smallest)
+ * @return two-tailed P-value (right or left, whichever is smallest)
  * 
  */
 public class CalcFisherExactTest extends HttpServlet  {
@@ -86,7 +86,7 @@ protected void doPost(HttpServletRequest httpServletRequest,
                 int c = Integer.parseInt(dataSet.split(" ")[2]);
                 int d = Integer.parseInt(dataSet.split(" ")[3]);    
                 FisherExact fisher = new FisherExact(a + b + c + d);
-                double pValue = fisher.getCumlativeP(a, b, c, d);
+                double pValue = fisher.getTwoTailedP(a, b, c, d);
                 result = result.concat(String.valueOf(pValue) + " ");                
             }
         }

core/src/main/java/org/mskcc/cbio/portal/stats/OddsRatio.java

@@ -87,7 +87,7 @@ public OddsRatio(ProfileDataSummary pDataSummary, String geneA, String geneB) {
 
         oddsRatio = ((double) (a * d)) / ((double) (b * c));
         FisherExact fisher = new FisherExact(a + b + c + d);
-        pValue = fisher.getCumlativeP(a, b, c, d);
+        pValue = fisher.getTwoTailedP(a, b, c, d);
         lowerConfidenceInterval = Math.exp(Math.log(oddsRatio) - 1.96 * (Math.sqrt(1 / (double) a
                 + 1 / (double) b + 1 / (double) c + 1 / (double) d)));
         upperConfidenceInterval = Math.exp(Math.log(oddsRatio) + 1.96 * (Math.sqrt(1 / (double) a
@@ -103,7 +103,7 @@ public double getOddsRatio() {
         return oddsRatio;
     }
 
-    public double getCumulativeP() {
+    public double getTwoTailedP() {
         return pValue;
     }
 

core/src/main/java/org/mskcc/cbio/portal/util/EnrichmentsAnalysisUtil.java

@@ -652,7 +652,7 @@ private double runFisherExactTest(HashMap<Integer, String> singleGeneCaseValueMa
             }
         }
         FisherExact fisher = new FisherExact(a + b + c + d);
-        return fisher.getCumlativeP(a, b, c, d);
+        return fisher.getTwoTailedP(a, b, c, d);
     }
 
     private String getCytoband(int geneticEntityId, String geneticProfileStableId) {

core/src/test/java/org/mskcc/cbio/portal/stats/TestFisherExact.java

@@ -39,7 +39,7 @@ public class TestFisherExact extends TestCase {
 
     public void testFisherExact() {
         FisherExact fisher = new FisherExact(43 + 2 + 17 + 7);
-        double p = fisher.getCumlativeP(43, 2, 17, 7);
+        double p = fisher.getTwoTailedP(43, 2, 17, 7);
         assertEquals(0.006653, p, 0.00001);
     }
 }

core/src/test/java/org/mskcc/cbio/portal/stats/TestOddsRatio.java

@@ -70,7 +70,7 @@ public void testFisherExact() throws IOException {
 
         OddsRatio oddsRatio = new OddsRatio(pDataSummary, "BRCA1", "BRCA2");
         double oddsRatioValue = oddsRatio.getOddsRatio();
-        double p = oddsRatio.getCumulativeP();
+        double p = oddsRatio.getTwoTailedP();
         assertEquals(0.16666, oddsRatioValue, 0.0001);
         assertEquals(0.0849, p, 0.0001);
         //System.out.println (oddsRatio.getRCommand());

docs/user-guide/faq.md

@@ -146,7 +146,7 @@ Group Comparison is a suite of analysis features which allows a user to compare
 - Other tabs
     - 2 groups
         - Continuous data: one-sided t-test
-        - Categorical data: one-sided Fisher's exact test
+        - Categorical data: two-sided Fisher's exact test
     - 3 or more groups
         - Continuous data: one-way ANOVA
         - Categorical data: Chi-squared test

persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java

@@ -1034,7 +1034,7 @@ public void getPatientStructuralVariantCountIncludeCustomDriverAnnotationsInclud
         alterationFilter.setStructuralVariants(true);
         alterationFilter.setMutationTypeSelect(Select.none());
         alterationFilter.setCnaTypeSelect(Select.none());
-        alterationFilter.setSelectedTiers(Select.byValues(List.of("Class 2")));
+        alterationFilter.setSelectedTiers(Select.byValues(Arrays.asList("Class 2")));
         alterationFilter.setIncludeUnknownTier(true);
         List<AlterationCountByGene> result = alterationMyBatisRepository.getPatientAlterationGeneCounts(
             svPatientIdToProfileId,
@@ -1049,7 +1049,7 @@ public void getPatientStructuralVariantCountIncludeCustomDriverAnnotationsExclud
         alterationFilter.setStructuralVariants(true);
         alterationFilter.setMutationTypeSelect(Select.none());
         alterationFilter.setCnaTypeSelect(Select.none());
-        alterationFilter.setSelectedTiers(Select.byValues(List.of("Class 2")));
+        alterationFilter.setSelectedTiers(Select.byValues(Arrays.asList("Class 2")));
         alterationFilter.setIncludeUnknownTier(false);
         List<AlterationCountByGene> result = alterationMyBatisRepository.getPatientAlterationGeneCounts(
             svPatientIdToProfileId,

service/src/main/java/org/cbioportal/service/util/AlterationEnrichmentUtil.java

@@ -132,7 +132,7 @@ public List<AlterationEnrichment> createAlterationEnrichments(Map<String, Pair<L
                         int alteredOnlyInQueryGenesCount = counts.get(0).getProfiledCount()
                             - counts.get(0).getAlteredCount();
 
-                        pValue = fisherExactTestCalculator.getCumulativePValue(alteredInNoneCount,
+                        pValue = fisherExactTestCalculator.getTwoTailedPValue(alteredInNoneCount,
                             counts.get(1).getAlteredCount(), alteredOnlyInQueryGenesCount,
                             counts.get(0).getAlteredCount());
                     } else {

service/src/main/java/org/cbioportal/service/util/FisherExactTestCalculator.java

@@ -40,4 +40,51 @@ public double getCumulativePValue(int a, int b, int c, int d) {
         }
         return p;
     }
+
+    public double getTwoTailedPValue(int a, int b, int c, int d) {
+
+        int min, i;
+        int n = a + b + c + d;
+        double p = 0;
+        double[] f = new double[n + 1];
+        f[0] = 0.0;
+
+        for (int j = 1; j <= n; j++) {
+            f[j] = f[j - 1] + Math.log(j);
+        }
+
+        double baseP = getPValue(a, b, c, d, f);
+//         in order for a table under consideration to have its p-value included
+//         in the final result, it must have a p-value less than the baseP, i.e.
+//         Fisher's exact test computes the probability, given the observed marginal
+//         frequencies, of obtaining exactly the frequencies observed and any configuration more extreme.
+//         By "more extreme," we mean any configuration (given observed marginals) with a smaller probability of
+//         occurrence in the same direction (one-tailed) or in both directions (two-tailed).
+
+        int initialA = a, initialB = b, initialC = c, initialD = d;
+        p += baseP;
+
+        min = (c < b) ? c : b;
+        for (i = 0; i < min; i++) {
+            double tempP = getPValue(++a, --b, --c, ++d, f);
+            if (tempP <= baseP) {
+                p += tempP;
+            }
+        }
+
+        // reset the values to their original so we can repeat this process for the other side
+        a = initialA;
+        b = initialB;
+        c = initialC;
+        d = initialD;
+
+        min = (a < d) ? a : d;
+        for (i = 0; i < min; i++) {
+            double pTemp = getPValue(--a, ++b, ++c, --d, f);
+            if (pTemp <= baseP) {
+                p += pTemp;
+            }
+        }
+        return p;
+    }
 }

service/src/test/java/org/cbioportal/service/util/AlterationEnrichmentUtilTest.java

@@ -101,8 +101,8 @@ public void createAlterationEnrichments() throws Exception {
 
         // START: for 2 groups
 
-        Mockito.when(fisherExactTestCalculator.getCumulativePValue(1, 1, 2, 0)).thenReturn(1.0);
-        Mockito.when(fisherExactTestCalculator.getCumulativePValue(2, 0, 0, 2)).thenReturn(0.3);
+        Mockito.when(fisherExactTestCalculator.getTwoTailedPValue(1, 1, 2, 0)).thenReturn(1.0);
+        Mockito.when(fisherExactTestCalculator.getTwoTailedPValue(2, 0, 0, 2)).thenReturn(0.3);
 
         List<AlterationEnrichment> result = alterationEnrichmentUtil.createAlterationEnrichments(
                 mutationCountsbyEntrezGeneIdAndGroup);